Yeah, I'm stumped too... I usually tend to put up the 3 charges, go face Nihilus, then put up the 4th charge (I don't know why). I've never had this problem before.
I don't know... I'd try loading an earlier game, one when you're still on Citadel Station or something (as much of a pain as this may be).
Yeah, I'm not much help, I know. <_<